Siege's End
by SageK
Summary: This story picks up where season 1 ended.
1. Default Chapter

"I'm going in."

Doctors Elizabeth Weir, Rodney McKay and Carson Beckett heard Major John Sheppard's quietly spoken words and knew their friend was about to sacrifice his life in an attempt to save Atlantis. Elizabeth stared grimly at the monitor on which they were tracking the Puddle Jumper's progress towards the Wraith ships, her fists clenched tightly. For once, Rodney was silent, eyes following the lone blue dot. Directly in front of the monitor, Carson was muttering under his breath, a prayer in a language few understood.

Unable to hold everything in, Elizabeth murmured, "John…oh…."

As the words left her mouth, another vessel streaked into sensor range.

"A ship!" Rodney burst, flinging himself onto a keyboard. "It just dropped out of hyperspace. It's the Daedalus. They're early."

"They're goin' after the Wraith," Carson added, pointing to the display.

"Major, hold back," Weir shouted into her radio. "Let's see if the Daedalus can turn the tide of the battle."

"Copy that," came Sheppard's reply. "I'm staying up here, just in case."

"Agreed," she said, watching at the Earth ship held it's own against their enemies.

At the console next to Rodney, the young marine looked up. "Ma'am, we've got data contact with the Daedalus. The General wants a report on our status down here."

Leaning over to the comm. station, she said, "We have Wraith in the city. Our defenses are taking a beating. Several of our people have been taken by the wraith darts. We are prepared to initiate self destruct should it prove necessary."

"Message transmitted," the young man said, watching his screen. "They're sending some ground troops."

"Daedalus just launched a fleet of F-302's," McKay announced as a whine from down in the Gate area announced the arrival of half a dozen heavily armed people. Another two whines deposited the same number of grim looking soldiers.

A petite woman waved her hand and the troops split into groups and hustled off to defend the city. The woman sprinted up the stairs. "General Hammond sends his regards," she said to Weir. "More Marines will be down shortly, but they're trying to get an insurgent team onto the hive ship where your people are being held, so they need the rings for a moment."

"People are ringing onto the hive ships?" Rodney asked, sounding both amazed and aghast. "that's suicide."

The woman nodded. "We don't abandon our people." She paused, than asked, "Any specific spots need added defense, so I can direct our re-enforcements that way."

"Here and here," Weir said, pointing to two areas on the city schematic. "That's where the Wraith took our people."

"Sands, Pound, your teams are heading into iffy areas. Heads up," the woman said into her radio.

"Copy that, Doc," came two replies and Weir glance at the woman.

The woman noticed. "Doctor Rebecca Ryan," she said by way of introducing herself. "We met at SGC, but that's neither here nor there. Have there been any breeches of main areas?"

Knowing now was not really a time to question this particular development, Weir, Rodney and Carson began to brief Dr. Ryan on their situation.

In high orbit, John Sheppard watched as the Daedalus and a squadron of smaller, maneuverable ships engaged the Wraith. He itched to join the fight, but knew it wasn't a good idea with the nuclear weapon sitting right behind him. If the battle seemed to be going in the Wraith's direction, then they would need him to commence the suicide run he had come up here to commit.

He saw several darts dock with one of the hive ships and, from the radio chatter being fed up to him from Atlantis, he could guess those were the ships that had taken their personnel.

"Atlantis, our people are aboard the smaller hive ship. Repeat, our people are aboard the smaller hive ship," he said, scrolling through the Puddle Jumpers functions, hoping there was something he could do.

"Major Sheppard, this is General Hammond aboard the Daedalus. We're putting a team over there now. I've been briefed on your plan. Continue to hold your position," a voice said over the comm. channel.

"Copy that sir," Sheppard replied, then couldn't help himself and asked. "Elizabeth, how are you holding up down there?"

"About as well as can be expected," came her strained reply. As soon as the words were out, gunfire and shouts sounded over the comm. link and Sheppard held his breath. "John! We're all right. A few Wraith just made it into command. They've been dealt with."

"Be careful," Sheppard almost pleaded with her. Though he knew he needed to hold his position, at least for now, a large part of him wanted to be down there defending his friends. Or at least participating in the dogfight happening right before his eyes.

As he watched, several of the smaller fighters commenced a straight run at a hive ship. Two of them pulled off a nice strafing run, but the other seemed to disappear into the hull of the Wraith vessel.

After a few minutes, it reappeared and rejoined it's fellows.

"What the hell is going on?" John grumbled. He hated sitting on his ass when the world seemed to be exploding all around him.

Aboard the Hive ship, Lieutenant Commander Jamison Kirkland pulled herself along on her elbows. After studying the enemy, with their large, broad builds, she figured they weren't likely to consider the slender ventilation shafts as a viable point of attack.

As soon as she had left the launch bay, her co-pilot, Captain Anthony Taylor, had rejoined the space battle. She and the others aboard the ship would have to find another way off the Hive ship. Soon after her arrival, she had slid into the air system and peered through the grates until she found an abandoned terminal. With it, Kirkland accessed information, such as the location of the cells and the engine room.

Her first stop was the engine room, where she planted several c4 charges with remote detonators. It was a fairly nerve wracking experience, as several Wraith seemed to stalk through the room at random intervals. But SEAL training tended to give one nerves of steel, so she completed her work and moved on.

Crouching in the air vents above the cells, she thumbed the remote, setting off the charges in the engine room. The ship rocked and alarms sounded. Knowing the chaos was likely to provide her with minimal cover, Kirkland dropped into the hall way and pounced on the console that controlled the cell doors.

A dozen men and women poured out of the cells, some of them recognizable from the briefings her team had been given on the Atlantis Expedition. Meeting the eyes of young Lieutenant Ford, she asked, "Is everyone mobile?"

He nodded, then glanced back into the group. "Peter's the worst off. He's been up here the

longest."

Kirkland followed his gaze to a man with ashen, bruised skin, who was leaning on an exotic young woman. His gaze was clear and alert however as he declared, "Let's get the hell out of here, please."

She nodded and handed her 9mm.'s and P90 off to Ford and two other marines, keeping her zat in hand. As the moved quickly, but cautiously down the hall, Ford whispered, "Ma'am, that explosion sounded big. We're going to have to watch for decompression."

"The engine room is several levels down from the launch bay we're headed for," she said, then zatted a Wraith that stepped into the hall. Another marine retrieved the stunned, and as they passed, Kirkland put two more blasts into it, leaving no trace.

The chaos caused by the destruction of the engine room was a better cover than Jamie had dared to hope for. The Wraith were obviously un used to having such stubborn and persistent enemies. Though several more Wraith were encountered on the way to the bay, they were quickly put down with either a zat or stunner blast. In fact, the most difficult part of their exit was figuring out hoe to get aboard the Wraith dart.

In the end, it was Teyla, the exotic Athosian woman, who found the hatch on the underside of the ship. The group made quick work of scrambling or being lifted into the ship and Kirkland dropped into the flight chair with a grimace. Damn thing was made for a 6'6" Wraith, not a 5'8" human.

Ford watched her scoot forward in her chair so as to reach all the controls. "Can you fly this thing, Ma'am?"

"I can fly anything, Lieutenant," she assured him, then proceeded to tap several panels and power up the craft. Before them, the launch bay doors parted and they shot out into space. "Daedalus and all F-302's, this is Commander Kirkland. I have our people. We are aboard the dart at the co-ordinates I'm sending you. Please be so kind as to not blow us out of the sky."

After a moment a voice crackled over her comm. Link. "It's good to hear your voice, Commander," General George Hammond said. "That ship you just left is the last hive. We were just waiting on you before finishing our job. Get yourselves into Bay 3."

"Respectfully, sir, I think that would be a bad idea," Kirkland said, feeling Ford's puzzled gaze on her profile. "I don't want to bring this craft aboard Daedalus. It could be rigged. I recommend doing a flyover of Atlantis. I can beam everyone but myself down, then land this thing on the mainland, a deserted area, and wait to be picked up."

There was a pause. "Agreed, Commander. Major Sheppard's Puddle Jumper will escort you to Atlantis, but you may have to wait a few hours for pick up."

"I'm sure I'll find something to do, sir."

"I await your debrief with baited breath. Have fun. Hammond out."

Ford raised a questioning eyebrow at Kirkland. "Fun, Ma'am?"

She grinned at him this time. "I'm going to have hours alone with an alien space craft. My inner geek is overjoyed," she told him. "and I'm Lieutenant Command Jamison Kirkland, by the way."

Before Ford could introduce himself or even make a quip about her name, the radio crackled again and a puddle jumper shimmered into view nearby. "You folks in the dart ready to go home?"

Kirkland waved Ford to the comm. "Yes, sir," he said, then glanced back at the others in the ship. "Major, Dr. Grodin's with us. He was on the hive ship."

"My God, how's he doing?" Sheppard's voice was heavy with relief.

"I'm alive, Major," Grodin said loudly from his seat where Teyla was inspecting his wounds. "So, bloody great!"

"Good to hear that, Peter," the Major called. "Now, Commander Kirkland…nice bird by the way."

"You should see my F-302," she quipped. "You want point?"

"You take it. I'll guard your six," he said, then paused. "You do know the scientists are going to be all over that dart the first opportunity they get."

"I know how to share my toys, Major," Kirkland smiled. "And I know all about scientists."


	2. Aftermath

The aftermath of the battle was, in some ways, more difficult to deal with than the conflict itself. The damage to the city was repairable, but the loss of personnel, military, scientists and Athosians, was significant. Elizabeth knew their names, had shared meals and stories with them and now they were gone. And there were still others in critical states, their lives in the capable, but human, hands of Carson and his staff.

Standing in command, she gazed down at the platform where the Gate rested and waited for her missing expedition members to reappear, courtesy of a stolen Wraith dart. In an almost blinding flash of blue, the group stood there. Elizabeth searched their faces, and when she saw one man, she drew up short. "Peter!"

At his computer, Rodney jerked upright and gaped as well before joining Weir in a scramble down to the others. They had thought Peter lost aboard the Ancient satellite when the Wraith destroyed it, but

here he more or less stood, arms slung around Teyla and Ford, woozy but very much alive.

"Dr. Weir, Rodney," he said, nodding to them, but wincing slightly at the movements. Rodney stopped short of hugging the man, but just barely. Lack of sleep did tend to make the man more emotional.

Before they could question him, Carson and a few of his larger, more intimidating assistants appeared and, in a flurry of activity rarely seen outside a county ER, triaged, then whisked the wounded away with shouted orders for all the others to get themselves down to the infirmary or there would be hell to pay.

Ford looked amused. He smiled at Weir and nodded to Carson's retreating back. "How can he be so calm about people with sucking wounds, but put a gun in his hand and he falls apart?"

"We're civilians, Lieutenant. We don't generally like guns," she said, knowing the young man did not really know anything but the military mentality. "You'll be glad to know, however, that he and Rodney both acquitted themselves well in defense of this city." She gestured to the side, where several marines were loading a deceased Wraith into a body bag.

When two of the enemy had come crashing into the gate room, gunfire had erupted all around Weir. A rain of bullets had put the creatures down and, with the smell of sulfur still in the air, she looked around and was startled. The guns clutched in the hands of every soldier weren't surprising, but seeing Rodney and Carson with weapons at ready was a shock.

With a nod, Ford said, "Then I'd better get down to the infirmary before the Doc comes after me." The young man then herded the rest of the survivors out of the gate room.

"Dr. Weir, all teams are reporting their sectors are clear," Rebecca Ryan said, trotting down the stairs from the upper deck. "Major Sheppard has just landed in the Jumper bay and General Hammond and Colonel Caldwell are waiting for your word to come down."

Still a bit unnerved, Weir nodded to the woman. "Tell them they may come down at their pleasure," she said, then glanced up to where John Sheppard was descending the stairs from the Jumper Bay. He sought her out and made eye contact, holding her gaze for several long moments. Before he had left on what they assumed would be a suicide mission, they had shared a similar communion and it had taken all their resolve to break away.

Watching him descend the stairs toward her, she couldn't help but feel an almost overwhelming sense of relief. _He's safe_. That thought echoed in her mind more than it should, but if she was honest with herself, John had long occupied a certain part of her heart. It wasn't love, but it was something that could become…something. But not now.

She shook her head slightly as he approached and smiled at him. "It's good to have you back, Major," Elizabeth said, then made a hand gesture to encompass all that was going on around them. "It looks like we'll be busy for a while."

For a quick moment, he grasped her arm, then nodded. "Yeah, but having the Daedalus up in orbit does give us a bit of a safety net. And McKay's going to go nuts over the dart that's just waiting for him on the mainland," Sheppard said, but sobered quickly. "How many did we lose?"

"Too many, at least a dozen," she told him, moving toward the stairs again.

McKay's face, pale and sweating, appeared from behind a consol. "Did you say a dart? An intact dart? Where?"

Blinking, Sheppard said, "You look like hell, McKay. You need some sleep."

"Sleep? I seem to vaguely recall what that is," the scientist said, then looked up in the direction of the Jumper Bay. "I should disarm that weapon."

Sheppard and Weir exchanged glances. "Let someone else do that, Rodney," Elizabeth said as she patted his shoulder. "Just relax for a bit or you're going to crash."

"Relax? Okay," McKay muttered, glancing around the area. Radek Zelenka had entered the room at some point and was speaking quietly with Ryan. He too looked dead on his feet. "I don't think Carson will give us any more stimulants."

"And that's probably a good thing," John said. "Get some rest. If you do, we'll go see that dart on the mainland."

"I'll be in my quarters then," Rodney said, rising quickly, swaying, then sitting down again. After a minute, he got to his feet, slowly and carefully.

Sheppard took his arm, then called over his shoulder. "Dr. Zelenka, you're off the clock too."

With a smile Weir watched as Atlantis's highest ranking military officer played sheep dog, herding the two exhausted but reluctant scientists off to their rooms. She knew he'd be back as soon as he deposited them in their rooms. After all, the General was on his way


	3. Ch 3

Despite the damage, Atlantis was even more impressive than George Hammond had expected. The city was huge and sprawling, with architecture more reminiscent of the Chrysler building than anything from ancient Earth history. And the wealth of technology, well he didn't need the science staff to tall him it was amazing.

"General Hammond, welcome to Atlantis," Dr. Elizabeth Weir greeted approaching with Major Sheppard at her side. As they stopped, Sheppard offered Hammond a respectful salute and received one in return.

"Doctor Weir, Major Sheppard, how are your people holding up?" he asked, knowing that the base had suffered some casualties and many injuries.

Weir crossed her arms over her chest. "Well, we're shaken, but everyone is comporting themselves admirably," she said with a nod to the men and women going about their jobs around them. "The people you sent down have been quite helpful."

"I should hope so," Colonel Steven Caldwell rumbled peering around at the activity.

Hammond smiled a bit. "Doctor, Major, this is Colonel Steven Caldwell. He'll be remaining here as commanding officer of the Daedalus."

Caldwell stepped forward took Weir's proffered hand before returning the Major's salute. "I look forward to working with the both of you," he said, then fell silent again.

The General tried not to smile. Caldwell was 100 United States Marine Corps and was _not _looking forward to working with a civilian and an admittedly unorthodox Air Force officer. Colonel Everett had been more Caldwell's style of soldier. Neither man got on that well with O'Neill, but they were effective Marines, which was part of the reason Hammond selected them for this mission.

Now Everett was gone, life drained out of him by one of the Wraith attacking the city. Which left Sheppard, who was, truth be told, too young and inexperienced to be ranking officer on the base. It couldn't really be helped though and the Major had proven himself more than capable. Now, in an odd way, he was the most experienced officer for the job.

"If you'll follow me gentlemen," Weir said, "We'll give you a full briefing."

As they followed her toward a conference room, the soldiers and scientists alike acknowledged them with salutes and nods. Hammond couldn't help but feel though, that the respect was directed more to Weir and Sheppard than himself or Caldwell. After all these people had been through together, it was only right.

Not five hours after John had finally fallen onto his bed, fully dressed and exhausted, someone was at his door. Groaning, he rolled over, hoping it was part of a bad dream. But then he heard the door slide open and heavy footsteps.

"Rodney, I don't think…."

"Don't think then."

_What the hell do McKay and Zelenka want _Sheppard thought, then weighed his options. One, he could jump up and scare the heck out of the two trespassers. But that would mean a lecture about heart attacks followed by whatever they were here for. Option two was to pretend he was still asleep and not waking up.

A finger jabbed itself into his shoulder. "Major?"

_Option two, it is._

Again Rodney poked him. "Major, wake up."

"Perhaps we should just leave him."

This time McKay grabbed his shoulder and shook. "Come on. I want to see that dart!"

_The dart. Crap._

Suddenly sitting upright with no warning had the suspected effect. Zelenka took a startled back step while McKay let out a yelp and hopped away.

"What the hell…you were faking!" McKay blurted, pointing and accusatory finger at Sheppard.

Stretching, John got to his feet and shuffled toward his bathroom. "Well, duh. You two aren't exactly stealthy. I'll be ready in five." And he closed the door on them.

The two scientists exchanged glances. Zelenka offered, "That went well."

After a moment, Rodney nodded. "It did."

Sitting in the co-pilot's chair beside Sheppard, Rodney watched as the mainland grew larger on the horizon as they approached. On the scanner, a small blip indicated where the dart had landed, quite a distance from the Athosian settlement. He was guiding the craft in the direction of the blip, as Sheppard had decided to catch another short nap on the journey.

Behind them he could hear Zelenka talking quietly with the three people who had come along for the ride. They were the teammates of the pilot who was with the dart and had wormed their way onto the trip, though McKay didn't know what a Marine Lieutenant, an Air Force Captain and a Doctor of…wait he didn't know.

"Hey, Ryan," he said, unable to recall the woman's first name. "What kind of doctor are you?"

"Anthropology and linguistics, with a dash of sociology and archaeology," she quipped, tugging the cap off of her reddish hair.

One of her teammates grinned, dark haired Lieutenant. "Yeah, Becky's our all purpose squishy science geek."

"Bite me."

"Gladly."

"You've been hanging with us too long, Becks, if the only response you could come up with was bite me," the blond Captain laughed teasingly.

Rodney chanced a glance back to see Ryan drawing herself up. "I'll have you know I have many crushing retorts at my disposal, but didn't want to confuse your poor little brains with polysyllabic words."

There was a pause, then the Lieutenant summed up his feelings very concisely. "Bite me."

Ryan and the Captain both burst out laughing, and even Zelenka joined in. The jolt as Rodney landed the Puddle Jumper cut their merriment short, however, and woke the Major.

Disoriented, John looked around, then focused on the controls. After a moment, he nodded to Rodney. "Not bad, McKay."

"What," he said, rising from his seat and gathering his pack, "you expected me to crash or something? If Carson can fly one of these things in a hurricane, I can certainly land one on a nice clear day."

As the rear door opened, the Captain-Taylor, that was his name- made a face. "Hot."

"And humid," Ryan agreed, stepping out onto the soil. "How far to the dart?"

Rodney glance over at the woman, and for the first time noticed how petite she was, maybe 160 cm, and that was wearing heavy boots. It took her two strides to keep up with one of Sheppard's, but she seemed used to the brisk pace. "About a mile," he told her. "In case the dart decides to self destruct, the Jumper should remain intact."


End file.
